Heat the oil in a large pan to medium heat and add the onions and jalapeno peppers. Cook them down about 5 minutes.
Add the garlic and cook another 30 seconds to 1 minute, until the garlic becomes fragrant.
Season the chicken thighs with salt and pepper, then add them to the pan. Cook them 2 minutes, then flip and cook 2 minutes more to lightly brown.
Process the tomato sauce and chipotles in adobo sauce in a food processor, then pour the mixture into the pan, covering the chicken.
Stir in the chili powder, cumin, Mexican oregano, and salt and pepper.
Bring to a quick boil, then reduce the heat and simmer for 30 minutes, or until the chicken is cooked through and easily pulls apart.
Remove the chicken and shred it with a couple of forks.
Return the chicken to the pan and simmer in the sauce another 5 minutes.
Serve with tortillas, tostadas, on torta buns, or in a bowl with all your favorite fixings.